In the Amazon basin, several species are restricted to or occur primarily in habitats along rivers. However, little is known about habitat occupancy over time and how seasonal fluctuations in the level of rivers affect bird species occurrence in floodplains. In this study, we verified if the occupancy and detection probability of 10 floodplain bird specialist species are related to 3 environmental variables considered to be important for floodplain birds: the number of Tessaria shrubs, the number of Cecropia trees, and the number of other tree species. We also tested if occupancy and detection probabilities changed among flood pulse seasons. Our study was conducted at 19 sampling sites in the Madeira River floodplain in Rondônia, Brazil, including sites impacted by the Santo Antonio dam. Sampling was done with autonomous recorders and subsequent development of semi-automatic identification models for each species. The best occupancy models show that the number of Tessaria shrubs was positively related to occupancy probability for 4 species: Black-and-white Antbird (Myrmochanes hemileucus), Parker's Spinetail (Cranioleuca vulpecula), White-bellied Spinetail (Mazaria propinqua), and Plain-crowned Spinetail (Synallaxis gujanensis). The number of Cecropia trees was positively correlated with the occupancy of a single species, the Spotted Tody-Flycatcher (Todirostrum maculatum). The number of other trees was positively correlated for White-browed Antbird (Myrboborus leucophrys), Peruvian Warbling-Antbird (Hypocnemis peruviana), and Band-tailed Manakin (Pipra fasciicauda). Occupancy probability is similar among sampling periods, which indicates that species remain onsite. The detection probability, however, varied in 9 of the 10 species, probably related to seasonal variation in vocal activity. This variation in detectability needs to be considered in bird surveys in floodplains. In addition, the classification of floodplain species according to the type of habitat specialization can help define the species most vulnerable to environmental changes, such as those caused by hydroelectric plants in the Amazon.